Index of /CVS_CONTENT/moby-live/Java/src/support/featureClient/

User's Manual ~~~~~~~~~~~~~ FeatuerClient version 1- November 08 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ =-=-=-=-=-=-=-=-=-=-=-=-=-=-= Welcome to the Moby FeatureClient! -=-=-=-=-=-=-=-=-=-=-=-=-=-=- ******************** TOC ******************** Section 1 ........................ Overview Section 2 ................. Getting Started Section 3 ....... Running the FeatureClient ******************** TOC ******************** Overview The FeatureClient is a extended MOBY client which provides the following features: 1. Calling services with the concrete objects (like AminoAcidSequence) instead of using the internal jmoby API 2. Service discovery based on service name or input/output definition (like return all services which consume an AGI locus code and return PMIDs) 3. Parallelization for multiple service calls 4. Using a timeout if the service does not return in that time 5. Calling a service once with possible different inputs Additionally it provides also the usual possibilities to call a moby service Getting Started 1. A Java Virtual Machine version 1.4.2 or later is required to run/use the FeatureClient 2. You can build the latest FeatureClient from the BioMoby cvs using on a Unix box /moby-live/Java/build.sh bindist-featureClient or on a windows box /moby-live/Java/build.bat bindist-featureClient The archive will be located at /moby-live/Java/docs/dist/, called featureClient.zip or featureClient-yyyy-mm-dd.tar.gz Copy it to a directory of your choice and unpack it there. The folder 'featureClient' should be created automatically. 3. Running / Using the FeatureClient: You can either use the FeatureClient to use it in your own project. Then just make sure that the FeatuerClient.jar and the required libraries (found in the 'lib' folder) are in your classpath. If you want to test the FeatureClient see the next section. Running the FeatureClient The following test programs are available to see how the client works. You can call one of them by using java -jar FeatureClient.jar <OPTION> where option can be one of the following: - SimpleSingleCall - calls one service once (maps an refseq identifier to an AGI locus code) - SimpleMultiCall - calls one service more than once (returns go information for a go term) - SingleCallDefinition - calls more services once which return for an AGI locus code pubmed ids - SingleCallWithParameters - calls one service once with parameters (to get orthologs from RefSeq) - SingleMultiServiceCall - calls two services once (get publications for AGI locus code) - ComplexSingleCall - calls one service once with a complex dataype (returns a protein sequence from a sequence) - MultCallByDefinition - calls more services more often which return for an AGI locus code mapman bins - MultiCallWithParameters - calls one service more often with parameters (to get orthologs from RefSeq) This shall give an impression what is possible with the client ! Andreas Groscurth andreas [dot] groscurth [at] gmail [dot] com